ArticleZoological letters2018
Draft genome of
Article in Zoological letters, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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Who cites it
21 citing papers in PubMed, 42 citations in OpenAlex.
- Stepwise emergence of recombination suppression precedes fissiparous asexuality in the planarian Schmidtea mediterranea.Nature communications · 2026Article
- Host-transposon mutualism supports regeneration in planarians.Developmental cell · 2026Article
- Article
- Red Midge Larvae Are an Invertebrate Alternative Diet to Beef Liver for Planarian Husbandry.Biomolecules · 2025Article
- tomoseqr: A Bioconductor package for spatial reconstruction and visualization of 3D gene expression patterns based on RNA tomography.PloS one · 2025Article
- A comparative analysis of planarian genomes reveals regulatory conservation in the face of rapid structural divergence.Nature communications · 2024Article
- Schild Analysis of the Interaction between Parthenolide and Cocaine Suggests an Allosteric Relationship for Their Effects on Planarian Motility.Biomolecules · 2024Article
- Isolation of planarian viable cells using fluorescence-activated cell sorting for advancing single-cell transcriptome analysis.Genes to cells : devoted to molecular & cellular mechanisms · 2023Article
- Genome Assembly of the Polyclad Flatworm Prostheceraeus crozieri.Genome biology and evolution · 2022Article
- Molecular characterization of a flatworm Girardia isolate from Guanajuato, Mexico.Developmental biology · 2022Article
- Article
- Collagen IV differentially regulates planarian stem cell potency and lineage progression.Proceedings of the National Academy of Sciences of the United States of America · 2021Article
- ACME dissociation: a versatile cell fixation-dissociation method for single-cell transcriptomics.Genome biology · 2021Article
- Alternative Animal Models of Aging Research.Frontiers in molecular biosciences · 2021Review
- Different classes of small RNAs are essential for head regeneration in the planarian Dugesia japonica.BMC genomics · 2020Article
- Dugesia japonica is the best suited of three planarian species for high-throughput toxicology screening.Chemosphere · 2020Article
- Screening of Potential Key Transcripts Involved in Planarian Regeneration and Analysis of Its Regeneration Patterns by PacBio Long-Read Sequencing.Frontiers in genetics · 2020Article
- CaCold Spring Harbor perspectives in biology · 2019Review
- JmjC Domain-Encoding Genes Are Conserved in Highly Regenerative Metazoans and Are Associated with Planarian Whole-Body Regeneration.Genome biology and evolution · 2019Article
- Calcium ions in the aquatic environment drive planarians to food.Zoological letters · 2019Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
13 authors at 8 institutions in 6 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundPlanarians are non-parasitic Platyhelminthes (flatworms) famous for their regeneration ability and for having a well-organized brain.
resultsTo obtain whole-genome information on this species and to study its gene regulatory networks, we extracted genomic DNA from 200 planarians derived from a laboratory-bred asexual clonal strain, and sequenced 476 Gb of data by second-generation sequencing. Kmer frequency graphing and fosmid sequence analysis indicated a complex genome that would be difficult to assemble using second-generation sequencing short reads. To address this challenge, we developed a new assembly strategy and improved the de novo genome assembly, producing a 1.56 Gb genome sequence (DjGenome ver1.0, including 202,925 scaffolds and N50 length 27,741 bp) that covers 99.4% of all 19,543 genes in the assembled transcriptome, although the genome is fragmented as 80% of the genome consists of repeated sequences (genomic frequency ≥ 2). By genome comparison between two planarian genera, we identified conserved non-coding elements (CNEs), which are indicative of gene regulatory elements. Transgenic experiments using
conclusionThis draft genome and CNE analysis will contribute to resolving gene regulatory networks in planarians. The genome database is available at: http://www.planarian.jp.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.